Circuit Motifs

Abstract

Gene circuit motifs are structural patterns associated with specific functions. In genetic networks, motifs are made of a small number of transcription units. A single transcription unit that contains a regulated promoter is sufficient to have either a negative or a positive feedback loop. Although very simple, they carry out important tasks such as speed up or slow down the circuit response time, achieve homeostatis (see Chap. 10
) or obtain bistability (see Chap. 6). The latter is an essential feature to build genetic memory devices. Like these feedback loops, most of the motifs presented in this chapter are based on transcription regulation. Logic operations (Boolean gates) can be carried out by controlling translation as well, either with structures such as riboswitches and ribozymes or via RNA interference (see Chap. 8). We considered as motifs also cell consortia. They are populations of cells where a given function emerges from the interactions of sets of cells devoted to different tasks. As we will see, digital circuits have been engineered as S. cerevisiae cell consortia, where some cells sense the inputs and other perform the logic operation and express a fluorescent output. Finally, we included among circuit motifs re-engineered pathways too. We will show that natural signaling pathways have been modified, both in eukaryotic and bacterial cells, to either respond to an input or express an output different from the original one. Complex circuits can potentially arise by the composition of all these basic motifs.